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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Mouse Phenome Database (MPD)
 
Resource Report
Resource Website
100+ mentions
Mouse Phenome Database (MPD) (RRID:SCR_003212) MPD experimental protocol, storage service resource, narrative resource, data repository, service resource, database, data or information resource Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list is used by: NIF Data Federation
is used by: Integrated Datasets
is used by: NIH Heal Project
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: Special Mouse Strains Resource
is related to: Vertebrate Trait Ontology
is related to: GenomeMUSter
has parent organization: Jackson Laboratory
NIDA ;
NHGRI HG003057;
NHLBI HL66611;
NIA AG025707;
NIA AG038070;
NIMH MH071984;
NIDA DA028420
PMID:24243846
PMID:22102583
PMID:18987003
PMID:17151079
Free, Freely available biotools:mpd, nif-0000-03160, r3d100010101 https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F http://www.jax.org/phenome SCR_003212 Mouse Phenome Database 2026-08-04 09:40:51 221
Database of Interacting Proteins (DIP)
 
Resource Report
Resource Website
100+ mentions
Database of Interacting Proteins (DIP) (RRID:SCR_003167) DIP data analysis service, analysis service resource, storage service resource, production service resource, service resource, data repository, database, data or information resource Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: re3data.org
is listed by: NIH Data Sharing Repositories
is listed by: bio.tools
is listed by: Debian
is related to: IMEx - The International Molecular Exchange Consortium
is related to: IMEx - The International Molecular Exchange Consortium
is related to: MPIDB
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: InteroPorc
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: NIH Data Sharing Repositories
is related to: PSICQUIC Registry
is related to: Agile Protein Interactomes DataServer
has parent organization: University of California at Los Angeles; California; USA
NIGMS PMID:14681454 Free, Available for download, Freely available OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F SCR_003167 , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) 2026-08-04 09:40:50 153
Piano
 
Resource Report
Resource Website
100+ mentions
Piano (RRID:SCR_003200) data processing software, software application, software resource, data analysis software Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. r, omics, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Chalmers University of Technology; Gothenburg; Sweden
has parent organization: Bioconductor
PMID:23444143 Free, Available for download, Freely available OMICS_01558, biotools:piano https://bio.tools/piano SCR_003200 2026-08-04 09:40:50 182
Solas
 
Resource Report
Resource Website
1+ mentions
Solas (RRID:SCR_003168) data processing software, source code, data analysis software, software resource, sequence analysis software, software application Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. r statistical package, rna seq, exon prediction, exon splicing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: R Project for Statistical Computing
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
Free, Available for download, Freely available biotools:solas, OMICS_01339 https://bio.tools/solas SCR_003168 2026-08-04 09:40:50 8
GenePattern
 
Resource Report
Resource Website
1000+ mentions
GenePattern (RRID:SCR_003201) GenePattern data processing software, software application, software resource, data analysis software A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is affiliated with: GenePattern Notebook
is related to: TIGRESS
has parent organization: Broad Institute
NCI ;
NIGMS
PMID:16642009 Free, Freely available biotools:genepattern, OMICS_01855, nif-0000-30654 https://bio.tools/genepattern SCR_003201 2026-08-04 09:40:50 1078
PIRSF
 
Resource Report
Resource Website
10+ mentions
PIRSF (RRID:SCR_003352) PIRSF narrative resource, standard specification, database, data or information resource A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: UniProtKB
has parent organization: Protein Information Resource
NHGRI U01-HG02712;
NSF DBI-0138188;
NSF ITR-0205470
PMID:19455212
PMID:14681371
Free, Freely available biotools:pirsf, nif-0000-03294, OMICS_01697 https://bio.tools/pirsf http://pir.georgetown.edu/pirsf/ SCR_003352 PIR SuperFamily, Protein Information Resource SuperFamily 2026-08-04 09:40:53 28
Cell Image Library (CIL)
 
Resource Report
Resource Website
10+ mentions
Cell Image Library (CIL) (RRID:SCR_003510) CIL image repository, storage service resource, data repository, service resource, database, data or information resource Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. microscopic image repository, microscopic video repository, cell animation repository, bio.tools is used by: NIF Data Federation
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: Cell Centered Database
is related to: Cell Centered Database
is related to: OME-TIFF Format
is related to: Integrated Manually Extracted Annotation
has parent organization: American Society for Cell Biology
has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR
has parent organization: University of California at San Diego; California; USA
is parent organization of: Biological Imaging Methods Ontology
NIGMS RC2 GM092708 PMID:34218671
PMID:34218673
Free, Freely available biotools:cellimagelibrary, nif-0000-37639, r3d100011601 http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J SCR_003510 Cell Image Library. CIL, Cell Image Library (CIL) 2026-08-04 09:40:55 19
Proteomics Identifications (PRIDE)
 
Resource Report
Resource Website
500+ mentions
Proteomics Identifications (PRIDE) (RRID:SCR_003411) PRIDE storage service resource, data repository, service resource, database, data or information resource Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools is used by: ProteomeXchange
is used by: BioSample Database at EBI
is recommended by: NIDDK Information Network (dkNET)
is listed by: Biositemaps
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: HUPO Proteomics Standards Initiative
is related to: ProteomeXchange
has parent organization: European Bioinformatics Institute
Wellcome Trust WT085949MA;
European Union FP7 LSHG-CT-2006-036814;
European Union FP7 260558;
European Union FP7 262067;
European Union FP7 202272;
BBSRC BB/I024204/1
PMID:23203882
PMID:19662629
Free, Available for download, Freely available nif-0000-03336, biotools:pride, r3d100011515 https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 SCR_003411 PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) 2026-08-04 09:40:54 642
Reactome
 
Resource Report
Resource Website
1000+ mentions
Reactome (RRID:SCR_003485) data analysis service, analysis service resource, production service resource, service resource, database, data or information resource Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list is used by: NIF Data Federation
is used by: DisGeNET
is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: WikiPathways
is related to: Pathway Commons
is related to: ConsensusPathDB
is related to: FlyMine
is related to: AmiGO
is related to: PSICQUIC Registry
is related to: Integrated Molecular Interaction Database
is related to: NCBI BioSystems Database
is related to: MOPED - Model Organism Protein Expression Database
is related to: KOBAS
is related to: PSICQUIC Registry
is related to: Pathway Interaction Database
is related to: hiPathDB - human integrated Pathway DB with facile visualization
is related to: Algal Functional Annotation Tool
has parent organization: Ontario Institute for Cancer Research
has parent organization: Cold Spring Harbor Laboratory
has parent organization: European Bioinformatics Institute
has parent organization: New York University School of Medicine; New York; USA
works with: PathwayMatcher
Ontario Research Fund ;
European Molecular Biology Laboratory ;
NHGRI P41 HG003751;
European Union FP6 ENFIN LSHG-CT-2005-518254;
NIGMS GM080223;
NIGMS R01 GM100039
PMID:21082427
PMID:21067998
Open source, Public, Freely available r3d100010285, nif-0000-03390, biotools:reactome https://bio.tools/reactome, https://doi.org/10.17616/R3V59P SCR_003485 Reactome Functional Interaction Network 2026-08-04 09:40:55 4282
L-Measure
 
Resource Report
Resource Website
10+ mentions
L-Measure (RRID:SCR_003487) LM data processing software, software resource, software application, image processing software, image analysis software, service resource A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools is listed by: 3DVC
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
has parent organization: Computational Neuroanatomy Group
Human Brain Project ;
NINDS R01 NS39600
PMID:18451794 Public nif-0000-00003, biotools:l-measure http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure SCR_003487 2026-08-04 09:40:55 30
Prodigal
 
Resource Report
Resource Website
1000+ mentions
Prodigal (RRID:SCR_011936) Prodigal simulation software, software application, software resource Software tool for protein coding gene prediction for prokaryotic genomes. is listed by: OMICtools
is listed by: Debian
is listed by: SoftCite
has parent organization: Oak Ridge National Laboratory
PMID:20211023 Free, Available for download, Freely available SCR_021246, OMICS_01493 https://sources.debian.org/src/prodigal/ http://prodigal.ornl.gov/ SCR_011936 , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm 2026-08-04 09:42:52 2985
MetAMOS
 
Resource Report
Resource Website
10+ mentions
MetAMOS (RRID:SCR_011914) MetAMOS data processing software, software application, software resource, workflow software A modular and open source metagenomic assembly and analysis pipeline. microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools is listed by: OMICtools
is listed by: Human Microbiome Project
is listed by: bio.tools
is listed by: Debian
is hosted by: GitHub
Open source, Available for download OMICS_01426, biotools:metamos https://github.com/marbl/metAMOS, https://bio.tools/metamos SCR_011914 2026-08-04 09:42:52 14
KisSplice
 
Resource Report
Resource Website
10+ mentions
KisSplice (RRID:SCR_011893) KisSplice data processing software, software application, software resource, data analysis software Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
DOI:10.1186/1471-2105-13-S6-S5 Free, Available for download, Freely available biotools:KisSplice, OMICS_01321 https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ SCR_011893 2026-08-04 09:42:52 20
ECHO
 
Resource Report
Resource Website
100+ mentions
ECHO (RRID:SCR_011851) ECHO data processing software, data analysis software, algorithm resource, software resource, sequence analysis software, software application Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:21482625
DOI:10.1101/gr.111351.110
Free, Available for download biotools:echo, OMICS_01102 https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ SCR_011851 ECHO: A reference-free short-read error correction algorithm 2026-08-04 09:42:52 310
CANGS
 
Resource Report
Resource Website
1+ mentions
CANGS (RRID:SCR_011837) CANGS data processing software, software application, software resource, data analysis software A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. windows, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
PMID:20180949 biotools:cangs, OMICS_01084 https://bio.tools/cangs SCR_011837 2026-08-04 09:42:52 1
JiffyNet
 
Resource Report
Resource Website
1+ mentions
JiffyNet (RRID:SCR_011954) data analysis service, simulation software, analysis service resource, software resource, software application, production service resource, service resource Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Yonsei University; Seoul; South Korea
National Research Foundation of Korea ;
Next-Generation BioGreen 21 Program
PMID:23685435 Free, Freely available OMICS_01548, biotools:jiffynet https://bio.tools/jiffynet SCR_011954 2026-08-04 09:42:53 1
sabre
 
Resource Report
Resource Website
100+ mentions
sabre (RRID:SCR_011843) sabre data processing software, software application, software resource, data analysis software Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
Free, Available for download, Freely available biotools:sabre, OMICS_01090 https://bio.tools/sabre SCR_011843 Systems Approach to Biomarker Research 2026-08-04 09:42:52 199
NGSmethDB
 
Resource Report
Resource Website
1+ mentions
NGSmethDB (RRID:SCR_012847) NGSmethDB storage service resource, data repository, service resource, database, data or information resource A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:20965971 OMICS_01844, biotools:ngsmethdb https://bio.tools/ngsmethdb SCR_012847 NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data 2026-08-04 09:43:06 9
MitoBreak
 
Resource Report
Resource Website
10+ mentions
MitoBreak (RRID:SCR_012949) MitoBreak storage service resource, data repository, service resource, database, data or information resource Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:24170808 Free, The community can contribute to this resource biotools:mitobreak, OMICS_01640 https://bio.tools/mitobreak SCR_012949 2026-08-04 09:43:06 10
minfi
 
Resource Report
Resource Website
100+ mentions
minfi (RRID:SCR_012830) minfi data processing software, data analysis software, software resource, software application, data visualization software Software tools for analyzing and visualizing Illumina''s 450k array data. Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: SWAN
has parent organization: Bioconductor
PMID:28035024 Free, Available for download, Freely available biotools:minfi, OMICS_00799, BioTools:minfi https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi SCR_012830 2026-08-04 09:43:05 390

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